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Crystal Structure of Mitochondrial Thioredoxin 3 from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ERU PDB ENTRY 1ERU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 0.2M ammonium sulfate, 0.1M sodium acetate, 8% PEG 4000,
15% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.6 52.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.569 α = 90 b = 49.569 β = 90 c = 94.423 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2005-12-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 25.38 99.66 0.074 14.8 17467
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.11 99 0.306 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ERU 2 25.38 16573 882 99.64 0.1741 0.17266 0.1775 0.19986 0.203 RANDOM 14.811
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.04 -0.02 -0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.124 r_dihedral_angle_4_deg 15.192 r_dihedral_angle_3_deg 14.245 r_dihedral_angle_1_deg 5.464 r_scangle_it 2.508 r_mcangle_it 2.077 r_scbond_it 1.668 r_angle_refined_deg 1.453 r_mcbond_it 1.271 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.124 r_dihedral_angle_4_deg 15.192 r_dihedral_angle_3_deg 14.245 r_dihedral_angle_1_deg 5.464 r_scangle_it 2.508 r_mcangle_it 2.077 r_scbond_it 1.668 r_angle_refined_deg 1.453 r_mcbond_it 1.271 r_nbtor_refined 0.302 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.101 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1656 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling CNS phasing